title: Features of Variable Number of Tandem Repeats in Yersinia pestis and the Development of a Hierarchical Genotyping Scheme.
abstract: Variable number of tandem repeats (VNTRs) that are widely distributed in the genome of Yersinia pestis proved to be useful markers for the genotyping and source-tracing of this notorious pathogen. In this study, we probed into the features of VNTRs in the Y. pestis genome and developed a simple hierarchical genotyping system based on optimized VNTR loci.
  
  
  
  Capillary electrophoresis was used in this study for multi-locus VNTR analysis (MLVA) in 956 Y. pestis strains. The general features and genetic diversities of 88 VNTR loci in Y. pestis were analyzed with BioNumerics, and a "14+12" loci-based hierarchical genotyping system, which is compatible with single nucleotide polymorphism-based phylogenic analysis, was established.
  
  
  
  Appropriate selection of target loci reduces the impact of homoplasies caused by the rapid mutation rates of VNTR loci. The optimized "14+12" loci are highly discriminative in genotyping and source-tracing Y. pestis for molecular epidemiological or microbial forensic investigations with less time and lower cost. An MLVA genotyping datasets of representative strains will improve future research on the source-tracing and microevolution of Y. pestis.
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China ; Laboratory Department, Navy General Hospital, Beijing, China.
authors.forename: Yanjun
authors.initials: Y
authors.lastname: Li
authors.forename: Yujun
authors.initials: Y
authors.lastname: Cui
authors.forename: Baizhong
authors.initials: B
authors.lastname: Cui
authors.forename: Yanfeng
authors.initials: Y
authors.lastname: Yan
authors.forename: Xianwei
authors.initials: X
authors.lastname: Yang
authors.forename: Haidong
authors.initials: H
authors.lastname: Wang
authors.forename: Zhizhen
authors.initials: Z
authors.lastname: Qi
authors.forename: Qingwen
authors.initials: Q
authors.lastname: Zhang
authors.forename: Xiao
authors.initials: X
authors.lastname: Xiao
authors.forename: Zhaobiao
authors.initials: Z
authors.lastname: Guo
authors.forename: Cong
authors.initials: C
authors.lastname: Ma
authors.forename: Jing
authors.initials: J
authors.lastname: Wang
authors.forename: Yajun
authors.initials: Y
authors.lastname: Song
authors.forename: Ruifu
authors.initials: R
authors.lastname: Yang
mesh_terms: D056426:Genetic Loci; D014644:Genetic Variation; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D020080:Tandem Repeat Sequences; D015010:Yersinia pestis / Q000145:classification / Q000235:genetics*